Wed Feb 15 08:55:02 PST 2012 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph_thinner.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Feb 15 2012 at 08:55:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6390350 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 0.6390350 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 343.2724 centred at (gu) : 90.37405 87.73377 91.95936 assigned negative charge : -337.7729 centred at (gu) : 90.20959 87.79229 91.90491 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6286 nv = 96 ne = 84 npr = 46967 no. pairs analyzed = 46967 no. exposed pairs = 2990 no. arc points = 21114 no. surface atoms = 996 nbur = 1295 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3254 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4480287E-09 1.9307095E-08 midg,1,midg; midg,igrid,midg 2.1286086E-08 1.1259267E-09 1,midg,midg; igrid,midg,midg -8.2635907E-09 2.5159242E-08 gauss-seidel spectral radius is 0.9872879 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 08:55:03 rms-change max change #iterations 0.1334734 24.15253 at 10iterations 1.2650839E-02 1.794403 at 20iterations 1.3154736E-03 0.2215729 at 30iterations 1.6221394E-04 2.9932022E-02 at 40iterations 3.6901682E-05 8.5964203E-03 at 50iterations finished qdiffx linear iterations at : 08:55:06 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 3.6901682E-05 8.5964203E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 08:55:06 3.271u 0.156s 0:03.96 86.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Feb 15 2012 at 08:55:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.917105 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 1.917105 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 343.2724 centred at (gu) : 91.12167 83.20109 95.87783 assigned negative charge : -337.7729 centred at (gu) : 90.62878 83.37670 95.71467 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67712 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21114 grid for indexing accessible points = 1.400000 m= 23141 mr = 45689 m= 3413 mr = 16373 m= 224 mr = 1974 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 30356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16945 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6390350 object centre at (A) : 2.985500 49.53150 26.66550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9317157E-04 3.2328866E-02 midg,1,midg; midg,igrid,midg 6.2501334E-02 2.2364639E-02 1,midg,midg; igrid,midg,midg -1.2659192E-02 2.3682719E-02 gauss-seidel spectral radius is 0.9986162 estimated iterations to convergence 213 setup time was (sec) 0.7800000 now iterating at: 08:55:07 rms-change max change #iterations 3.922673 166.2621 at 10iterations 1.820548 68.85056 at 20iterations 0.8454216 27.98692 at 30iterations 0.3930847 13.49208 at 40iterations 0.1827285 6.275860 at 50iterations 8.5078150E-02 2.973718 at 60iterations 3.9518554E-02 1.301724 at 70iterations 1.8468276E-02 0.5849304 at 80iterations 8.6012296E-03 0.3023987 at 90iterations 3.9967806E-03 0.1366215 at 100iterations 1.8780789E-03 6.0523987E-02 at 110iterations 8.8920508E-04 4.0061951E-02 at 120iterations finished qdiffx linear iterations at : 08:55:14 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 8.8920508E-04 4.0061951E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 08:55:15 7.259u 0.242s 0:08.53 87.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Feb 15 2012 at 08:55:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.875658 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -19.36900 25.34000 ymin,ymax (A): 21.67700 77.38600 zmin,zma (A): 2.006000 51.32500 x,y,z range (A): 44.70900 55.70900 49.31900 scale (grids/A): 2.875658 object centre (A): 2.985500 49.53150 26.66550 number of atom coordinates read : 2291 total number of charged atoms : 2154 net assigned charge : 5.500013 assigned positive charge : 343.2724 centred at (gu) : 91.68240 79.80145 98.81682 assigned negative charge : -337.7729 centred at (gu) : 90.94319 80.06501 98.57199 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 156303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21114 grid for indexing accessible points = 1.400000 m= 75943 mr = 111044 m= 26053 mr = 60623 m= 5860 mr = 20167 m= 988 mr = 4258 m= 84 mr = 670 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 68426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 17231 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.917105 object centre at (A) : 2.985500 49.53150 26.66550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5751084E-02 0.3031358 midg,1,midg; midg,igrid,midg 0.6016659 0.5187285 1,midg,midg; igrid,midg,midg -9.3559183E-02 0.2268587 gauss-seidel spectral radius is 0.9992603 estimated iterations to convergence 290 setup time was (sec) 1.470000 now iterating at: 08:55:17 rms-change max change #iterations 9.405260 392.8851 at 10iterations 5.536446 148.1701 at 20iterations 3.233522 111.0141 at 30iterations 1.877966 43.71971 at 40iterations 1.090498 25.24089 at 50iterations 0.6311893 13.80547 at 60iterations 0.3640922 7.408612 at 70iterations 0.2105862 4.229219 at 80iterations 0.1211902 2.677923 at 90iterations 6.9856875E-02 1.347689 at 100iterations 4.0299281E-02 0.7746735 at 110iterations 2.3121709E-02 0.4566956 at 120iterations 1.3287960E-02 0.2814980 at 130iterations 7.6606534E-03 0.1517792 at 140iterations 4.4022053E-03 8.4785461E-02 at 150iterations 2.5416883E-03 5.2553177E-02 at 160iterations 1.4633959E-03 3.0342102E-02 at 170iterations 8.4687967E-04 1.5922546E-02 at 180iterations finished qdiffx linear iterations at : 08:55:27 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 8.4687967E-04 1.5922546E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 08:55:28 11.922u 0.239s 0:12.50 97.2% 0+0k 0+0io 0pf+0w